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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0964 | |||||||||
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Title | Cryo-EM structure of a pre-60S ribosomal subunit - state preA | |||||||||
![]() | Cryo-em structure of a human pre-60S ribosomal subunit state - preA | |||||||||
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![]() | 60S / pre-60S / pre-ribosome / human 60S / human pre-ribosome / NMD3 / human NMD3 / RIBOSOME | |||||||||
Function / homology | ![]() negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / negative regulation of G2/M transition of mitotic cell cycle / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation ...negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / negative regulation of G2/M transition of mitotic cell cycle / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of G1 to G0 transition / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of translation involved in cellular response to UV / ribosomal protein import into nucleus / protein-DNA complex disassembly / 90S preribosome assembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / GAIT complex / A band / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / regulation of glycolytic process / regulation of reactive oxygen species metabolic process / middle ear morphogenesis / negative regulation of cell-cell adhesion / cytoplasmic side of rough endoplasmic reticulum membrane / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / homeostatic process / response to aldosterone / negative regulation of DNA replication / positive regulation of dendritic spine development / macrophage chemotaxis / lung morphogenesis / ribosomal large subunit binding / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / positive regulation of signal transduction by p53 class mediator / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / blastocyst development / cellular response to actinomycin D / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / protein localization to nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / ribosomal subunit export from nucleus / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / translation initiation factor activity / cytosolic ribosome / embryo implantation / ossification / cellular response to interleukin-4 / assembly of large subunit precursor of preribosome / negative regulation of cell migration / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of translation / regulation of signal transduction by p53 class mediator / cytosolic ribosome assembly / innate immune response in mucosa / mRNA 3'-UTR binding / skeletal system development / DNA damage response, signal transduction by p53 class mediator / sensory perception of sound / response to insulin / cellular response to gamma radiation / transcription coactivator binding / bone development / mRNA 5'-UTR binding / cellular response to type II interferon / Regulation of expression of SLITs and ROBOs / positive regulation of protein binding / cytoplasmic ribonucleoprotein granule / rRNA processing / osteoblast differentiation / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to UV / antibacterial humoral response / ribosome biogenesis Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
![]() | Liang X / Zuo M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural snapshots of human pre-60S ribosomal particles before and after nuclear export. Authors: Xiaomeng Liang / Mei-Qing Zuo / Yunyang Zhang / Ningning Li / Chengying Ma / Meng-Qiu Dong / Ning Gao / ![]() Abstract: Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which ...Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 38.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 65.4 KB 65.4 KB | Display Display | ![]() |
Images | ![]() | 87.7 KB | ||
Filedesc metadata | ![]() | 16 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 417.4 KB | Display | ![]() |
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Full document | ![]() | 416.9 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lssMC ![]() 0948C ![]() 0963C ![]() 0978C ![]() 6lqmC ![]() 6lsrC ![]() 6lu8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-em structure of a human pre-60S ribosomal subunit state - preA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Cryo-EM structure of a human pre-60S ribosomal subunit state - preA
+Supramolecule #1: Cryo-EM structure of a human pre-60S ribosomal subunit state - preA
+Macromolecule #1: Nucleolar GTP-binding protein 2
+Macromolecule #3: Nucleolar GTP-binding protein 1
+Macromolecule #5: Eukaryotic translation initiation factor 6
+Macromolecule #6: Probable ribosome biogenesis protein RLP24
+Macromolecule #8: Zinc finger protein 593
+Macromolecule #9: 60S ribosomal protein L3
+Macromolecule #10: 60S ribosomal protein L29
+Macromolecule #11: 60S ribosomal protein L4
+Macromolecule #12: 60S ribosomal protein L30
+Macromolecule #13: 60S ribosomal protein L34
+Macromolecule #14: 60S ribosomal protein L7a
+Macromolecule #15: 60S ribosomal protein L35
+Macromolecule #16: 60S ribosomal protein L9
+Macromolecule #17: 60S ribosomal protein L36
+Macromolecule #18: 60S ribosomal protein L27a
+Macromolecule #19: 60S ribosomal protein L37
+Macromolecule #20: 60S ribosomal protein L11
+Macromolecule #21: 60S ribosomal protein L38
+Macromolecule #22: 60S ribosomal protein L39
+Macromolecule #23: 60S ribosomal protein L13
+Macromolecule #24: Translation machinery-associated protein 16
+Macromolecule #25: 60S ribosomal protein L14
+Macromolecule #26: 60S ribosomal protein L15
+Macromolecule #27: 60S ribosomal protein L13a
+Macromolecule #28: 60S ribosomal protein L36a
+Macromolecule #29: 60S ribosomal protein L37a
+Macromolecule #30: 60S ribosomal protein L17
+Macromolecule #31: 60S ribosomal protein L18
+Macromolecule #32: 60S ribosomal protein L19
+Macromolecule #33: 60S ribosomal protein L18a
+Macromolecule #34: 60S ribosomal protein L21
+Macromolecule #35: 60S ribosomal protein L22
+Macromolecule #36: 60S ribosomal protein L23
+Macromolecule #37: 60S ribosomal protein L23a
+Macromolecule #38: 60S ribosomal protein L26
+Macromolecule #39: 60S ribosomal protein L27
+Macromolecule #40: 60S ribosomal protein L31
+Macromolecule #41: 60S ribosomal protein L32
+Macromolecule #42: 60S ribosomal protein L28
+Macromolecule #43: 60S ribosomal protein L8
+Macromolecule #44: 60S ribosomal protein L35a
+Macromolecule #45: 60S ribosomal protein L6
+Macromolecule #46: 60S ribosomal protein L7
+Macromolecule #47: 60S ribosomal protein L5
+Macromolecule #48: Protein LLP homolog
+Macromolecule #2: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #7: 28S rRNA
+Macromolecule #49: MAGNESIUM ION
+Macromolecule #50: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10277 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING |